in reply to BioPerl: Best Gene Ontology API

You should maybe have a look at the Bioconductor R packages Category and GOstats as well. There are many annotation databases in Bioconductor and they are well maintained. So you can use basically the same code for enrichment tests of other annotation databases, for example KEGG, PFAM, Chromosome Bands etc. And it's easy to map ids (affy, illumina,..) to Entrez for example.

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Re^2: BioPerl: Best Gene Ontology API
by BioLion (Curate) on Aug 23, 2010 at 17:38 UTC

    Yes - this is what the SeqAnswers guys thought too - R/bioConductor seems to be much more on the ball with GO analysis compared to Perl. I still love her though.

    Just a something something...
      Check out the Bioconductor case studies book (By Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon). There's a whole chapter about this. The code is also available online. It will save you lots of time...

        Will do! Thanks!

        Just a something something...